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Contact Info

Skills

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Jarrod J. Scott

an old-school naturalist using new-school tech

I study microbial diversity. My holistic approach spans marine & terrestrial systems to better understand how a collection of simple organisms coalesce into complex communities & how the structure of these communities affect host biology, biogeochemical cycles, & ecosystem-level processes. I also want to make research more accessible & exciting, transparent & reproducible. To that end, I use & teach open-source tools to create web products that communicate science more effectievly.

Current Appointment

STRI/Moore Foundation Postdoctoral Fellow

Smithsonian Tropical Research Institute

Panama

2017 -

  • Transisthmian microbial ecology of coral reefs & mangrove ecosystems in the Western Atlantic & the Tropical Eastern Pacific of Panama.

Education

PhD Microbiology

University of Wisconsin–Madison

Madison, Wisconsin USA

2011 - 2006

  • Microbial ecology of fungus growing insects

BSc Aquatic Biology, Minor in Archaeology

University of Texas–Austin

Austin, Texas USA

2002 - 1998

Prior Research Positions

Postdoctoral Research Associate

Bigelow Laboratory for Ocean Sciences

East Boothbay, Maine USA

2016 - 2012

Graduate Fellow

University of Wisconsin–Madison

Madison, Wisconsin USA

2011 - 2010

Predoctoral Fellow

Smithsonian Tropical Research Institute

Gamboa, Panama

2010 - 2009

Research Technician

University of Texas–Austin

Austin, Texas USA

2005 - 2002

Marine Field Experience

Research Expeditions to Isla Coiba

Smithsonian Tropical Research Institute

Isla Coiba, Panama

2020 - 2017

5 expeditions over the past 3 years

Use this link to learn more about Isla Coiba.

R/V Revelle & ROV Jason II (cruise RR1413)

Submarine Ring of Fire - Ironman Cruise

Mariana BackArc Basin

2014

November 23 – December 21

All research cruises from 2012 - 2014 were to study the microbial ecology of deep-sea hydrothermal systems, specifically iron-oxidizing communities.

R/V Atlantic Explorer (cruise AE1410)

Chief Scientist Training Cruise

Barbados to Bermuda

2014

May 31 – June 10

R/V Thompson, ROV Jason II, & AUV Sentry (cruise TN293)

FeMo Deep Iron Eaters

Lo’ihi Seamount, Hawaii

2013

March 4 – April 1

R/V Knorr & ROV Jason II (cruise KN209-02)

Woods Hole Oceanographic Institution

Mid-Atlantic Ridge

2012

October 16 – November 14

I’ve also worked on a lobster boat in Maine & a seine boat in Alaska.

R/V Longhorn

University of Texas-Austin

Gulf of Mexico

2001

Terrestrial Field Experience

Microbial Ecology of Fungus-Growing Ants

Smithsonian Tropical Research Institute

Panama

2010 - 2008

  • Four expeditions to Panama
  • 15-month residency at STRI
  • Field & lab experiments with fungus-growing ants

A lot of my field experience in terrestrial systems is on fungus-growing ants in the Neotropics.

Biogeography of Fungus-Growing Ants

University of Texas

Mexico & Panama

2004 - 2001

Multiple field expeditions to understand the biogeography of fungus-growing ants & their fungal symbionts.

Molecular Ecology of Cichlids in Northern Mexico

University of Texas

Coahuila, Mexico

2001 - 2000

Molecular analysis of cichlid fish endemic to aquifer fed pools of the Cuatro Cienegas Basin.

Mayan Archaeological Surveys

University of Texas

Northwestern Belize

2000

Extensive surveys & excavations of Mayan archaeological sites in lowland tropical rain forests.

Recent Teaching Experience

Course Instructor

STRI-McGill Tropical Biology Field Course

Panama

2020

  • Guide project design & implementation.
  • Reproducible analytical workflows using R Markdown.
  • Assist with field work.
  • Natural history of neotropical marine & terrestrial ecosystems.

Field sites incl. Barro Colorado Island, Ft Sherman Canopy Crane, Pipeline Road Forests, Agua Salud & Isla Coiba.

I teach the way I learn. My goal is to create a venue where students can be curious, get their hands dirty, make mistakes, & explore. I’m here to help students see what’s possible, not tell them what to do.

Marine Biology Instructor

STRI-McGill Tropical Biology Field Course

Isla Coiba, Panama

2019

  • Guide project design & implementation.
  • Assist with field work.
  • Snorkeling class for inexperienced students.

Click here for the course blog & here for the course website.

Additional Training & Certifications

PADI Rescue Diver Certification Course

Panama Dive School

Bocas del Toro, Panama

2018

PADI Advanced Open Water Diver Certification Course

Panama Dive School

Bocas del Toro, Panama

2017

PADI Open Water Diver Certification Course

Panama Dive School

Bocas del Toro, Panama

2017

PoreCamp

University of Exeter Sequencing Center

Penryn, England

2016

1-week hands-on training bootcamp on deploying Oxford Nanopore’s portable sequencing platform, the MinION.

Click here to learn more.

Complex Systems Summer School

Santa Fe Institute

Santa Fe, New Mexico USA

2015

4-week intensive course on complex systems.

Click here for the 2015 CSSS proceedings.

UNOLS Chief Scientist Training Cruise

The University-National Oceanographic Laboratory System

Barbados to Bermuda.

2014

2-week course on how to effectively plan for, acquire, utilize, & report on time at sea for multi-disciplinary research & education.

Click here for the final report from the 2014 UNOLS training cruise.

Fire Fighter I & II. NFPA 1001-2006

Southern Maine Community College

Portland, Maine USA

2013

Year-long training course for Fire Fighter I & II Certification.

Microbial Diversity Course

Marine Biological Labs

Woods Hole, Massachusetts USA

2007

6-week intensive course. Cultivating, & isolating diverse microbes. Molecular & computational analyses.

Click here to learn more.

Marine Botany & the Biology of Fish

University of Texas Marine Science Institute.

Port Aransas, Texas USA

2001

Archaeological Field Techniques

The Programme for Belize Archaeological Project

Orange Walk District, Belize

2000

Intensive field course on Mayan art, architecture, & iconography.

Learn more on the course website.

Fellowships

Smithsonian Institution Genomics Postdoctoral Fellowship

declined

Panama

2014 - 2012

Wisconsin Distinguished Graduate Fellowship

College of Agriculture & Life Science

University of Wisconsin–Madison

2011 - 2010

Smithsonian Institution Predoctoral Fellowship

Smithsonian Tropical Research Institute

Panama

2010 - 2009

Peer Reviewed Publications

Intestinal microbes: an axis of functional diversity among large marine consumers

Proceedings of the Royal Society B: Biological Sciences In Press

N/A

2020

Scott JJ, Adam TC, Duran A, Burkepile DE, Rasher DB.

Click here for the project website & reproducible workflows from this paper.

A Genus definition for Bacteria and Archaea based on a standard genome relatedness index

mBio 11(2020):e02475-19

N/A

2020

Barco RA, Garrity GM, Scott JJ, Amend JP, Nealson KH, Emerson D.

Editor’s Pick

Biological rejuvenation of iron oxides in bioturbated marine sediments.

The ISME Journal. 12(2018):1389-1394.

N/A

2018

Beam JP, Scott JJ, McAllister SM, Chan CS, McManus J, Meysman FJ, Emerson D.

Bringing microbial diversity into focus: high‐resolution analysis of iron mats from the Lō‘ihi Seamount.

Environmental Microbiology. 19(2017):301-316.

N/A

2017

Scott JJ, Glazer BT, Emerson D.

Physiological and ecological implications of an iron-or hydrogen-oxidizing member of the Zetaproteobacteria, Ghiorsea bivora, gen. nov., sp. nov.

The ISME Journal. 11(2017):2624-2636.

N/A

2017

Mori JF, Scott JJ, Hager KW, Moyer CL, Küsel K, Emerson D.

Biogeography of mutualistic fungi cultivated by leafcutter ants.

Molecular Ecology. 26(2017):6921-6937.

N/A

2017

Mueller UG, Ishak HD, Bruschi SM, Smith CC, Herman JJ, Solomon SE, Mikheyev AS, Rabeling C, Scott JJ, Cooper M, Rodrigues A.

In situ estimates of iron-oxidation and accretion rates for iron-oxidizing bacterial mats at Lō’ihi Seamount.

Deep Sea Research Part I: Oceanographic Research Papers. 126(2017):31-39.

N/A

2017

Emerson D, Scott JJ, Leavitt A, Fleming E, Moyer C.

Exploring the “SHARKCANO”: biogeochemical observations of the Kavachi Submarine Volcano (Solomon Islands).

Oceanography. 29(2016):160-169.

N/A

2016

Phillips BT, Dunbabin M, Henning B, Howell C, DeCiccio A, Flinders A, Kelley KA, Scott JJ, Albert S, Carey S, Tsadok R.

Microbial iron mats at the Mid-Atlantic Ridge and evidence that Zetaproteobacteria may be restricted to iron-oxidizing marine systems.

PLoS One. 10(2015):e0119284.

N/A

2015

Scott JJ, Breier JA, Luther III GW, Emerson D.

Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores.

Nature Communications. 6(2015):8285.

N/A

2015

Sanders JG, Beichman AC, Roman J, Scott JJ, Emerson D, McCarthy JJ, Girguis PR.

Microbial iron oxidation in the arctic tundra and its implications for biogeochemical cycling.

Applied & Environmental Microbiology. 81(2015):8066-8075.

N/A

2015

Emerson D, Scott JJ, Benes J, Bowden WB.

Unique honey bee (Apis mellifera) hive component-based communities as detected by a hybrid of phospholipid fatty-acid and fatty-acid methyl ester analyses.

PloS One. 10(2015):e0121697.

N/A

2015

Grubbs KJ, Scott JJ, Budsberg KJ, Read H, Balser TC, Currie CR.

Convergent bacterial microbiotas in the fungal agricultural systems of insects.

mBio. 5(2014):e02077-14.

N/A

2014

Aylward FO, Suen G, Biedermann PH, Adams AS, Scott JJ, Malfatti SA, del Rio TG, Tringe SG, Poulsen M, Raffa KF, Klepzig KD.

Using in situ voltammetry as a tool to identify and characterize habitats of iron-oxidizing bacteria: from fresh water wetlands to hydrothermal vent sites.

Environmental Science: Processes & Impacts 16(2014):2117-2126.

N/A

2014

MacDonald DJ, Findlay AJ, McAllister S, Barnett JM, Hredzak-Showalter P, Krepski ST, Cone SG, Scott JJ, Bennett SK, Chan CS, Emerson D, GW Luther III.

Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens.

Applied & Environmental Microbiology 79(2013):3770-3778.

N/A

2013

Aylward FO, Burnum-Johnson KE, Tringe SG, Teiling C, Tremmel DM, Moeller JA, Scott JJ, Barry KW, Piehowski PD, Nicora CD, Malfatti SA.

A phylogenetic analysis of the phylum Fibrobacteres.

Systematic & Applied Microbiology. 36(2013):376-382.

N/A

2013

Jewell KA, Scott JJ, Adams SM, Suen G.

Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens.

The ISME Journal. 6(2012):1688-701.

N/A

2012

Aylward FO, Burnum KE, Scott JJ, Suen G, Tringe SG, Adams SM, Barry KW, Nicora CD, Piehowski PD, Purvine SO, Starrett GJ.

The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle.

PLoS Genetics. 7(2011):e1002007.

N/A

2011

Suen G, Teiling C, Li L, Holt C, Abouheif E, Bornberg-Bauer E, Bouard P, Caldera EJ, Cash E, Cavanaugh A, Denas O, Elhaik E, Fav MJ, Gadau J, Gibson JD, Graur D, Grubbs KJ, Hagen DE, Harkins TT, Helmkampf M, Hu H, Johnson BR, Kim J, Marsh SE, Moeller JA, Muoz-Torres MC, Murphy MC, Naughton MC, Nigam S, Overson R, Rajakumar R, Reese JT, Scott JJ Smith CR, Tao S, Tsutsui ND, Viljakainen L, Wissler L, Yandell MD, Zimmer F, Taylor J, Slater SC, Clifton SW, Warren WC, Elsik CG, Smith CD, Weinstock GM, Gerardo NM, Currie CR.

Microbial community structure of leaf-cutter ant fungus gardens and refuse dumps.

PloS One 5(2010):e9922.

N/A

2010

Scott JJ, Budsberg KJ, Suen G, Wixon DL, Balser TC, Currie CR.

An insect herbivore microbiome with high plant biomass-degrading capacity.

PLoS Genetics. 6(2010): e1001129.

N/A

2010

Suen G, Scott JJ, Aylward FO, Adams SM, Tringe SG, Pinto-Tomás AA, Foster CE, Pauly M, Weimer PJ, Barry KW, Goodwin LA.

Monoculture of leafcutter ant gardens.

PLoS One. 5(2010):e12668.

N/A

2010

Mueller UG, Scott JJ, Ishak HD, Cooper M, Rodrigues A.

Polymorphic microsatellite markers for the symbiotic fungi cultivated by leaf cutter ants (Attini, Formicidae).

Molecular Ecology Resources. 9(2009):1391-1394.

N/A

2009

Scott JJ, Weskin MK, Cooper M, Mueller UG.

Mycangimycin, a polyene peroxide from a mutualist Streptomyces.

Organic Letters. 11(2009):633-636.

N/A

2009

Oh DC, Scott JJ, Currie CR, Clardy J.

Bionectriol A, a polyketide glycoside from the fungus Bionectria sp. associated with the fungus-growing ant, Apterostigma dentigerum.

Tetrahedron Letters. 50(2009):6834-6837.

N/A

2009

Freinkman E, Oh DC, Scott JJ, Currie CR, Clardy J.

Bacterial protection of beetle-fungus mutualism

Science. 2008 322(5898):63.

N/A

2008

Scott JJ, Oh DC, Yuceer MC, Klepzig KD, Clardy J, Currie CR.

See accompanying Perspective: Bugs Bugs. Berenbaum MR, Eisner T. 2008. Science. 322:52-53.

Disclaimer

The source code for this cv is available here. I made it with the R package pagedown and help from the Internet, especially this repo.

Last updated on 2020-03-01.